AgiMicroRna and Replicates
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Karthik K N ▴ 200
@karthik-k-n-5092
Last seen 8.3 years ago
Dear Members, Do we need replicates to carry out analysis with AgiMicroRna package in bioconductor? I have one control and one treated samples. Can I go ahead with AgiMicroRna with these two datasets? Thank you. -- Karthik K.N [[alternative HTML version deleted]]
AgiMicroRna AgiMicroRna • 909 views
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@richard-friedman-513
Last seen 8.3 years ago
Dear Karthik, I am pretty sure that AgiMicroRna will normalize one treated and one control. The problem comes later in terms of the reproducibility of the effect, or to phrase it differently, whether the observed effect is a general statement about the population of treatments and controls. In more specific terms, the subsequent LIMMA analysis will not compute a p-value. With hopes that this helps, Rich ------------------------------------------------------------ Richard A. Friedman, PhD Associate Research Scientist, Biomedical Informatics Shared Resource Herbert Irving Comprehensive Cancer Center (HICCC) Lecturer, Department of Biomedical Informatics (DBMI) Educational Coordinator, Center for Computational Biology and Bioinformatics (C2B2)/ National Center for Multiscale Analysis of Genomic Networks (MAGNet) Room 824 Irving Cancer Research Center Columbia University 1130 St. Nicholas Ave New York, NY 10032 (212)851-4765 (voice) friedman at cancercenter.columbia.edu http://cancercenter.columbia.edu/~friedman/ "School is an evil plot to suppress my individuality" Rose Friedman, age15 On Jun 14, 2012, at 5:51 AM, Karthik K N wrote: > Dear Members, > > Do we need replicates to carry out analysis with AgiMicroRna package > in > bioconductor? I have one control and one treated samples. Can I go > ahead > with AgiMicroRna with these two datasets? > > Thank you. > > -- > Karthik K.N > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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Dear Rich, Thanks a lot for your reply. I am just worried because somewhere I remember reading that LIMMA can't be used without replicates ( in case of mRNA microarray analysis); so just wanted to check if it is the same with AgiMicroRna package also. Also, Do you think it is a good idea to carry out GeneSpring analysis upon the data analyzed by biocondcutor? Will it give any statistically more reliable output that using either of them alone? Also, since the data from bioconductor has already normalized, if we again give this as an input file for genespring and go on with analysis, then do we need to do normalization step again in GeneSpirng? Won't this be a double-normalization? I am new to R/Bioconductor, so any suggestions from you will be extremely helpful. Thanks a lot, Karthik On Thu, Jun 14, 2012 at 7:08 PM, Richard Friedman < friedman@cancercenter.columbia.edu> wrote: > Dear Karthik, > > I am pretty sure that AgiMicroRna will normalize one treated and > one control. The problem comes later in terms of the reproducibility > of the effect, or to phrase it differently, whether the observed effect > is a general statement about the population of treatments and controls. > In more specific terms, the subsequent LIMMA analysis will not > compute a p-value. > > With hopes that this helps, > Rich > ------------------------------**------------------------------ > Richard A. Friedman, PhD > Associate Research Scientist, > Biomedical Informatics Shared Resource > Herbert Irving Comprehensive Cancer Center (HICCC) > Lecturer, > Department of Biomedical Informatics (DBMI) > Educational Coordinator, > Center for Computational Biology and Bioinformatics (C2B2)/ > National Center for Multiscale Analysis of Genomic Networks (MAGNet) > Room 824 > Irving Cancer Research Center > Columbia University > 1130 St. Nicholas Ave > New York, NY 10032 > (212)851-4765 (voice) > friedman@cancercenter.**columbia.edu <friedman@cancercenter.columbia.edu> > http://cancercenter.columbia.**edu/~friedman/<http: cancercenter.co="" lumbia.edu="" ~friedman=""/> > > "School is an evil plot to suppress my individuality" > > Rose Friedman, age15 > > > > > > > > > > > > On Jun 14, 2012, at 5:51 AM, Karthik K N wrote: > > Dear Members, >> >> Do we need replicates to carry out analysis with AgiMicroRna package in >> bioconductor? I have one control and one treated samples. Can I go ahead >> with AgiMicroRna with these two datasets? >> >> Thank you. >> >> -- >> Karthik K.N >> >> [[alternative HTML version deleted]] >> >> ______________________________**_________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.e="" thz.ch="" mailman="" listinfo="" bioconductor=""> >> Search the archives: http://news.gmane.org/gmane.** >> science.biology.informatics.**conductor<http: news.gmane.org="" gmane="" .science.biology.informatics.conductor=""> >> > > -- Karthik K.N Cancer Discovery Biology Laboratory Division of Molecular Medicine Amrita Center for Nanosciences and Molecular Medicine Amrita Institute of Medical Sciences AIMS-Ponekkara (P.O), Kochi Cochin, Kerala - 682 041 +91-484-280 1234 x 8720 +91-9400193907 [[alternative HTML version deleted]]
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Dear Karthik, On Jun 14, 2012, at 9:45 AM, Karthik K N wrote: > Dear Rich, > > Thanks a lot for your reply. I am just worried because somewhere I > remember reading that LIMMA can't be used without replicates ( in > case of mRNA microarray analysis); so just wanted to check if it is > the same with AgiMicroRna package also. I think that LIMMA can be used without replicates but it cannot give you a p-value. I suggest a minimum of 3 biological replicates per sample. > > Also, Do you think it is a good idea to carry out GeneSpring > analysis upon the data analyzed by biocondcutor? Will it give any > statistically more reliable output that using either of them alone? I do not know how GeneSpring normalizes Agilent MicroRNA data but AgiMicroRna is the best way to normalize such data described in the open literature of which I am aware. The statistical methods in LIMMA are more reliable than those in GeneSpring in general. However with only one replicate of each condition neither program can give a p- value, only a log2FC. You can get the same result in an excel spreadsheet, > > Also, since the data from bioconductor has already normalized, if we > again give this as an input file for genespring and go on with > analysis, then do we need to do normalization step again in > GeneSpirng? Won't this be a double-normalization? I haven't used GeneSpring for a long time. I am not sure what it will do to your data. If you only have one replicate you might consider using AgiMicroRNA to normalize and Excel to compute the log2FC. Best wishes, Rich > > I am new to R/Bioconductor, so any suggestions from you will be > extremely helpful. > > Thanks a lot, > > Karthik > > > On Thu, Jun 14, 2012 at 7:08 PM, Richard Friedman <friedman at="" cancercenter.columbia.edu=""> > wrote: > Dear Karthik, > > I am pretty sure that AgiMicroRna will normalize one treated > and > one control. The problem comes later in terms of the reproducibility > of the effect, or to phrase it differently, whether the observed > effect > is a general statement about the population of treatments and > controls. > In more specific terms, the subsequent LIMMA analysis will not > compute a p-value. > > With hopes that this helps, > Rich > ------------------------------------------------------------ > Richard A. Friedman, PhD > Associate Research Scientist, > Biomedical Informatics Shared Resource > Herbert Irving Comprehensive Cancer Center (HICCC) > Lecturer, > Department of Biomedical Informatics (DBMI) > Educational Coordinator, > Center for Computational Biology and Bioinformatics (C2B2)/ > National Center for Multiscale Analysis of Genomic Networks (MAGNet) > Room 824 > Irving Cancer Research Center > Columbia University > 1130 St. Nicholas Ave > New York, NY 10032 > (212)851-4765 (voice) > friedman at cancercenter.columbia.edu > http://cancercenter.columbia.edu/~friedman/ > > "School is an evil plot to suppress my individuality" > > Rose Friedman, age15 > > > > > > > > > > > > On Jun 14, 2012, at 5:51 AM, Karthik K N wrote: > > Dear Members, > > Do we need replicates to carry out analysis with AgiMicroRna package > in > bioconductor? I have one control and one treated samples. Can I go > ahead > with AgiMicroRna with these two datasets? > > Thank you. > > -- > Karthik K.N > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > > -- > Karthik K.N > Cancer Discovery Biology Laboratory > Division of Molecular Medicine > Amrita Center for Nanosciences and Molecular Medicine > Amrita Institute of Medical Sciences > AIMS-Ponekkara (P.O), Kochi > Cochin, Kerala - 682 041 > +91-484-280 1234 x 8720 > +91-9400193907 >
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Dear Rich, Thank you so much for your inputs. Regards, Karthik On Thu, Jun 14, 2012 at 7:24 PM, Richard Friedman < friedman@cancercenter.columbia.edu> wrote: > Dear Karthik, > > > On Jun 14, 2012, at 9:45 AM, Karthik K N wrote: > > Dear Rich, >> >> Thanks a lot for your reply. I am just worried because somewhere I >> remember reading that LIMMA can't be used without replicates ( in case of >> mRNA microarray analysis); so just wanted to check if it is the same with >> AgiMicroRna package also. >> > > I think that LIMMA can be used without replicates but it cannot give you a > p-value. I suggest > a minimum of 3 biological replicates per sample. > > > >> Also, Do you think it is a good idea to carry out GeneSpring analysis >> upon the data analyzed by biocondcutor? Will it give any statistically more >> reliable output that using either of them alone? >> > > I do not know how GeneSpring normalizes Agilent MicroRNA data but > AgiMicroRna is the best way to > normalize such data described in the open literature of which I am aware. > The statistical methods in LIMMA are more reliable than those in > GeneSpring in general. However > with only one replicate of each condition neither program can give a > p-value, only a log2FC. > You can get the same result in an excel spreadsheet, > > > > >> Also, since the data from bioconductor has already normalized, if we >> again give this as an input file for genespring and go on with analysis, >> then do we need to do normalization step again in GeneSpirng? Won't this be >> a double-normalization? >> > > I haven't used GeneSpring for a long time. I am not sure what it will do > to your data. > If you only have one replicate you might consider using AgiMicroRNA to > normalize and Excel to > compute the log2FC. > > Best wishes, > Rich > > > > > >> I am new to R/Bioconductor, so any suggestions from you will be extremely >> helpful. >> >> Thanks a lot, >> >> Karthik >> >> >> On Thu, Jun 14, 2012 at 7:08 PM, Richard Friedman <friedman@cancercenter.>> **columbia.edu <friedman@cancercenter.columbia.edu>> wrote: >> Dear Karthik, >> >> I am pretty sure that AgiMicroRna will normalize one treated and >> one control. The problem comes later in terms of the reproducibility >> of the effect, or to phrase it differently, whether the observed effect >> is a general statement about the population of treatments and controls. >> In more specific terms, the subsequent LIMMA analysis will not >> compute a p-value. >> >> With hopes that this helps, >> Rich >> ------------------------------**------------------------------ >> Richard A. Friedman, PhD >> Associate Research Scientist, >> Biomedical Informatics Shared Resource >> Herbert Irving Comprehensive Cancer Center (HICCC) >> Lecturer, >> Department of Biomedical Informatics (DBMI) >> Educational Coordinator, >> Center for Computational Biology and Bioinformatics (C2B2)/ >> National Center for Multiscale Analysis of Genomic Networks (MAGNet) >> Room 824 >> Irving Cancer Research Center >> Columbia University >> 1130 St. Nicholas Ave >> New York, NY 10032 >> (212)851-4765 (voice) >> friedman@cancercenter.**columbia.edu <friedman@cancercenter.columbia.edu> >> http://cancercenter.columbia.**edu/~friedman/<http: cancercenter.c="" olumbia.edu="" ~friedman=""/> >> >> "School is an evil plot to suppress my individuality" >> >> Rose Friedman, age15 >> >> >> >> >> >> >> >> >> >> >> >> On Jun 14, 2012, at 5:51 AM, Karthik K N wrote: >> >> Dear Members, >> >> Do we need replicates to carry out analysis with AgiMicroRna package in >> bioconductor? I have one control and one treated samples. Can I go ahead >> with AgiMicroRna with these two datasets? >> >> Thank you. >> >> -- >> Karthik K.N >> >> [[alternative HTML version deleted]] >> >> ______________________________**_________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.e="" thz.ch="" mailman="" listinfo="" bioconductor=""> >> Search the archives: http://news.gmane.org/gmane.** >> science.biology.informatics.**conductor<http: news.gmane.org="" gmane="" .science.biology.informatics.conductor=""> >> >> >> >> >> -- >> Karthik K.N >> Cancer Discovery Biology Laboratory >> Division of Molecular Medicine >> Amrita Center for Nanosciences and Molecular Medicine >> Amrita Institute of Medical Sciences >> AIMS-Ponekkara (P.O), Kochi >> Cochin, Kerala - 682 041 >> +91-484-280 1234 x 8720 >> +91-9400193907 >> >> > -- Karthik K.N Cancer Discovery Biology Laboratory Division of Molecular Medicine Amrita Center for Nanosciences and Molecular Medicine Amrita Institute of Medical Sciences AIMS-Ponekkara (P.O), Kochi Cochin, Kerala - 682 041 +91-484-280 1234 x 8720 +91-9400193907 [[alternative HTML version deleted]]
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@steve-lianoglou-2771
Last seen 3 months ago
United States
Hi, On Thu, Jun 14, 2012 at 5:51 AM, Karthik K N <karthikuttan at="" gmail.com=""> wrote: > Dear Members, > > Do we need replicates to carry out analysis with AgiMicroRna package in > bioconductor? I have one control and one treated samples. Can I go ahead > ewith AgiMicroRna with these two datasets? It depends on what you mean by "need". I suspect that it is *technically* possible to carry out an analysis without replicates so that at the end of day you get *some* results. In that sense, you might not "need" replicates. If by "need" you mean that you want results that you can have some faith in, then yes: you need replicates ... always. -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology ?| Memorial Sloan-Kettering Cancer Center ?| Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact
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Dear Steve, Thank you for your reply. I have done microarray experiments with pooled samples instead of replicates. I wanted to know if there is any technical difficulty in AgiMicroRna if we have no replicates. Thanks, Karthik On Thu, Jun 14, 2012 at 7:32 PM, Steve Lianoglou < mailinglist.honeypot@gmail.com> wrote: > Hi, > > On Thu, Jun 14, 2012 at 5:51 AM, Karthik K N <karthikuttan@gmail.com> > wrote: > > Dear Members, > > > > Do we need replicates to carry out analysis with AgiMicroRna package in > > bioconductor? I have one control and one treated samples. Can I go ahead > > ewith AgiMicroRna with these two datasets? > > It depends on what you mean by "need". > > I suspect that it is *technically* possible to carry out an analysis > without replicates so that at the end of day you get *some* results. > In that sense, you might not "need" replicates. > > If by "need" you mean that you want results that you can have some > faith in, then yes: you need replicates ... always. > > -steve > > -- > Steve Lianoglou > Graduate Student: Computational Systems Biology > | Memorial Sloan-Kettering Cancer Center > | Weill Medical College of Cornell University > Contact Info: http://cbio.mskcc.org/~lianos/contact > -- Karthik K.N Cancer Discovery Biology Laboratory Division of Molecular Medicine Amrita Center for Nanosciences and Molecular Medicine Amrita Institute of Medical Sciences AIMS-Ponekkara (P.O), Kochi Cochin, Kerala - 682 041 +91-484-280 1234 x 8720 +91-9400193907 [[alternative HTML version deleted]]
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